I've executed exonerate with a dataset, but it isn't producing any output despite the fact I set --showvulgar yes. I've seen a previous thread on this Problems with Exonerate output. However, this doesn't solve my problem as a file is printed that simply repeats the commands I've used and nothing more. Another thread on a different site had the answer of "exonerate -h". Sadly, the exonerate "help" and manual do not indicate on option for creating an output, other than telling the program what kind of output you want.

This just the basic set of commands I've used. As I've said, I've also tried suggestions from the other pages. This is running on a cluster, if that information is helpful.

EDIT: I've also tried running this on my own computer just now and nothing even prints to the screen in terminal, other than exonerate repeats my commands and appears to keep running in the background. No output (intermediate or otherwise) is produced.